Target Sequencing of Japanese Soybean (Glycine max) Cultivars by Sequence Capture

The soybean genome sequence is the ultimate tool for elucidating the genes involved in expression of many economical, nutritional and agronomic traits. The whole shotgun sequence assembly of Glycine max var. Williams 82 revealed a genome size of 950 Mb (http://www.phytozome.org/soybean.php). In order to facilitate more efficient analysis of Japanese soybean cultivars, we sequenced the genome of cultivar Enrei using the Roche/454 GS-FLX Titanium sequencing platform. The sequence data can be accessed via DAIZUbase (http://daizu.dna.affrc.go.jp), which also contains the Williams 82 genome sequence, BAC end sequences, physical map, DNA marker information, and a BLAST search system. The high-quality Enrei genome sequence allows for accurate comparison of single nucleotide polymorphisms (SNPs), insertions and deletions (In/Dels) with the Williams 82 genome sequence. We used these resources to develop molecular markers among Japanese domestic soybean cultivars. The NimbleGen sequence capture method based on Enrei BAC end sequences was used to compare various regions on the genome of several cultivars. Approximately 40 Mb regions from each whole genome were concentrated and sequenced. The resulting sequence data were filtered using BAC end sequences and mapped in silico into the Williams82 genome. The SNPs between the Williams82 and Enrei genome were then used as reference in detecting SNPs among local soybean cultivars. These SNP data will be incorporated in DAIZUbase soon and can be used in breeding for improved soybean cultivars. This work is supported by a grant from the Ministry of Agriculture, Forestry and Fisheries of Japan (Genomics for Agricultural Innovation, SOY1001).